Three Years Later
by tessa626
Summary: It's been three years since Destiny's crew went into stasis. Dr Rush has a lot on his mind, keeping the ship is in working order so that they don't all die, but there are other things that haunt him as well. Rated M for possible future smut & violence.
1. Chapter 1

**A.N. Hey, this is my first fic, so I'd really appreciate reviews. Go easy on me though, I'm a newbie. If I get enough positive feedback, I might write more. I noticed there weren't to many Dr Rush/Mandy Perry fics so I thought I'd try something out. If I do end up writing more, I'll be trying for some smut, so fingers crossed for good reviews! Enjoy!**

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><p>Dr. Nicholas Rush sat in the command chair of <em>Destiny'<em>s empty bridge rubbing his temple tiredly. He gazed around the dim, quiet room. Three years. It had been three whole years. The rest of the crew had staggered off to their quarters for some much needed sleep after three years of waiting in stasis. He was too restless to sleep. That at least was the same. He knew he needed it, but he couldn't bring himself to leave the bridge. He ran his fingers gently over the controls closest to him, bringing displays and diagnostics to life. Everything appeared to be in order. He sighed and rubbed his eyes as he began writing a program to run a check on all the main systems.

_I'll go to bed when I've finished this program and sleep for a few hours. Just have to finish this first… _His thoughts trailed off as he felt a brush of cool air across the back of his neck. He stopped, looked over his shoulder, and narrowed his eyes. _If Eli is back at his kinos…_ but it wasn't a kino. There was nothing there.

_Alright, time for bed. I'm imagining things. I can continue this in a few hours._ He left the program he was working on and headed out of the bridge and into the silent, empty halls of _Destiny's_ interior. His shoes made a sharp clacking noise against the metal floor, echoing eerily around the quiet corridor.

_Nicholas_. A breath of cool air across his back carrying his name made him stiffen. He stopped and looked around, eyes narrowed. It was entirely possible the life support systems were acting up. Three years with no one tending to it was bound to take a toll. Once he was sure no one was in the corridor with him he continued on to his room cautiously.

The door to his room opened and he breathed a small sigh of relief. Everything was just as he'd left it. He quickly removed his clothing and crawled onto the bed, remembering how uncomfortable they actually were. He lay on his back for a while, staring up at the ceiling, picking up where he'd left off on problems before going into stasis. Eventually, he rolled to his side and fell asleep.

_He stood outside a door in an empty hallway on Destiny, the cold metal of the corridor making him shiver. A sense of dread was slowly coiling in his stomach as he stared at the closed door. He knew what he'd find, but he also knew he had to do it. He reached and pushed the button to open the door. He stepped through and looked down at the floor and felt his throat tighten at the sight. Amanda Perry, broken and bleeding, sprawled out on the floor of her quarters. He trembled and knelt slowly by her side, picking her up and cradling her cold, limp body. He rocked back and forth for a moment, holding her to him._

_He froze as cold laughter echoed to him from somewhere in Destiny's interior. He looked up and saw Simeon standing in the corridor outside the room. He was smiling as he took off running into the labyrinth of passageways. Rush laid Mandy's body down as gently as he could and got to his feet, giving her one last look as he took off after the killer. He ran for what seemed like miles, always just out of reach. He'd run around a corner and see his target disappear around another, and always the laughter echoed around, taunting him. Finally, he ran down a hall that seemed to lead to somewhere brighter. He rounded the corner and found himself outside._

_The sun, glaringly bright, shone down on the desolate landscape. Rush looked around him, frantically searching the desert now surrounding him. He glanced down and found he held a gun, low on ammo. Shots fired around him and he dove for cover. Rush's breath was harsh in his ears as he leaned against the rocky outcrop he was using for cover. He took a breath, quickly spinning around, letting a shot loose before ducking to safety again, narrowly avoiding getting shot himself. He was trembling; rage and grief sweeping through him. Another shot rang out, hitting the rocks just above his head. An explosion off to his right and approaching thunder gave him a momentary triumph. The screams of the murderer caused a grim smile to spread across his haggard face. Once the thunder had passed he stood over the murderer, now beaten into the dust. Rage filled him as he saw the man was still smiling, still mocking him. He raised his gun coldly and shot him, but the smile remained. The smile wouldn't die, and it was soon joined by laughter. The laughter got louder and louder until it filled his head, and he knew that that no matter what he did, he'd never get her back…_

Rush started awake with a gasp, trembling and sitting bolt upright, the laughter still echoing in his mind. He forced himself to calm down, lying back on the pillows, taking deep, harsh breaths through his nose. His efforts were in vain, as his breaths turned to sobs and he shook, arms wrapped around his torso clutching himself. He curled up on his side and tried to muffle his sobs in the pillow. He was so tired, so lost.

A cool hand touched his forehead and soothed him, allowing him to relax. He opened his eyes, but couldn't see anything in the darkness of his room through the haze of tears. He made as if to say something, but a cool finger brushed his lips and a breathy _shhhh_ quieted him. He leaned back, letting his mind relax, the horror of his dream leaving him. Just before he nodded off, his mind grasped at what made the voice and the presence so familiar, but failed as he finally slipped into a deep and dreamless sleep.


	2. Chapter 2

"Rush!" Rush groaned and rolled over, burying his head in the pillow. A moment later there was a loud banging on his door followed by Colonel Young's voice. "Rush open up! We've got flashing red lights on all the consoles, and I don't want to explode!" Rush sighed and rolled off the bed, painfully stretching as he stood. Those beds certainly did a number on his back. "Rush!"

"Coming!" He threw on a shirt and went to the door. He was out and past Colonel Young as soon as the door opened, leaving him to follow in Rush's wake. "I take it the radios aren't charged yet."

"You would have ignored the call anyway."

Rush looked over his shoulder at the Colonel. "Good morning to you too." The Colonel caught up with Rush and they walked briskly down the corridor. "Is Eli still asleep?"

"Yes, TJ's with him in the infirmary. He was in pretty rough shape when he went into stasis and the pod wasn't as gentle in its transitions as it could have been."

"Well let me know when he's up and ready to work. I may need him soon."

"I'll send him up as soon as I've debriefed him. I want a full account on record of what happened after we all went to sleep. Actually, you'll probably want to hear it too."

"If I can be spared from whatever this is."

Rush strode onto the bridge flanked by Colonel Young. Alarms and flashing lights off the consoles greeted him as he paused on the upper platform. He looked down to see Brody and Volker scrambling back and forth between the consoles. Rush sighed. It felt as though he'd never left.

"Alright you two, what have we got?" Rush came down and sat in the command chair, pulling up the programs and ships functions that seemed to be having trouble.

"Multiple ships functions are down, life support is one of the only remaining functioning systems, and it looks like that won't last for long. We need to refuel soon or we'll be set adrift with no air or heat." Rush frowned at Brody. Did the man enjoy bad news?

"Do you want to tell me why everything was fine when I left this last night? And can we turn those BLOODY ALARMS OFF?!" Volker fumbled with some buttons on one of the consoles and the sound cut out. "Now, when I left everything here last night, it was fine. Would you like to tell me what transpired in the meantime?"

Volker and Brody looked at each other uncertainly. "Well…" Volker started and trailed off. Brody spoke up.

"We were just having a look at the systems to see what was what and I saw there was a program running."

"And your first instinct was to, what, start playing with it? How old are you?" Brody tried to protest but Rush cut him off. "Oh, for the love of God, just label the buttons you pressed since coming in here, and I'll figure out what you did myself."

"But we can—"

"No, not now. You've done enough. I'll call you if I need you, but for now, out." Brody looked as if he was about to say something else, but stopped with a sigh and left the bridge with Volker.

After a moment or two of silence, Colonel Young followed them. "Radio if you need anything Rush." He didn't answer, already deep into trying to find what they did to set off the alarms. He expected some sort of glitch in his program that they had caused, but there was nothing to be found. In fact, all the systems looked to be absolutely fine. He kept looking, but it was getting harder and harder to concentrate. He was still tired after the nightmare, and getting woken up in the middle of a deep slumber didn't help matters.

Slowly, his eyes began to slide closed and he drifted off to sleep…

_He was standing in his home back on Earth, the home he had left years ago for the project that would land him several billion light years away. He looked around slowly. Afternoon sunlight was filtering in through the windows illuminating the room in a soft glow. There was a woman sitting on the couch with her back to him. She appeared to be reading. He walked slowly around her until he could see her face. _

_It was Amanda Perry, unbroken and in the peak of health. She seemed to glow as she looked up from her book and smiled at him warmly. He smiled too, but there was something at the back of his mind telling that this was a bit off. He looked down at the book she was reading. The book it was filled with the glyphs and symbols of the Ancients, some of which he was sure he had seen before but couldn't remember what they meant. Rush looked back up at Amanda and stiffened as their eyes caught. Instead of the lovely blue eyes he knew, hers were the deep black of space with a sprinkling of stars. As he stared, the room around him darkened and disappeared, and began to fall into those dark, star filled eyes._

Rush started awake, sitting up with a groan and much creaking of joints. He frowned and rubbed his eyes, glancing at the clock on a nearby display. He blinked and looked at the display again. He'd been asleep for several hours and after a quick mental calculation, figured they'd be dropping out of FTL in about four hours. There was nothing else he could see that he needed to do right away, especially as tired as he was, so he started to get up to leave when he saw her. He froze.

"Mandy?" He whispered in shock. There, in the center of the bridge, stood Dr. Amanda Perry. She smiled shyly.

"Hello Nick. Long time no see." Rush swallowed a few times, coming slowly towards her, hurt confusion, and relief all vying for position on his face. "Months in a quarantined file and three years on a powered down ship…" She paused. "It's good to see you Nick."

Rush gave a start and seemed to find his voice. "Yeah, it's great to see you too, but…I don't understand. I thought you were gone."

She smiled sadly. "For a while I did too."

"How−"

"You should really hear the full story from Eli. Most of it's his anyway."

Rush's face darkened. "He's the one responsible for this−"

"Don't blame him Nick. He saved your life and probably mine too!" Neither said anything for a while, both a little taken aback by Mandy's outburst. Then Rush brought up what had occurred the night before.

"So…if this is real, and hallucinations are entirely possible explanations for all this, then that dream just now…"

"Yes that was me."

"And last night too?"

"Yes. It took me longer than I'd expected to find the right psychic protocols, but I did manage to help you back to sleep after that nightmare." Rush closed his eyes for a moment and pushed away the images of her broken body in his arms.

"Psychic protocols? You have access to that part of _Destiny's_ programming?"

She nodded. "Yes, I've had access to just about everything after Eli…" She stopped and looked away.

"Mandy, what did Eli do?"

"Promise you won't be angry with him. He was doing what he thought was right, and really, it was."

"Mandy, I−"

"Promise."

"Yes, alright, I promise."

"He's awake in the infirmary. Colonel Young is on his way, you can meet him there."

"Thank you." He reached out to her as if to touch her cheek but stopped just short, unsure if he could bear not being able to feel her ever again.

"It's okay," she whispered and tilted her head so her cheek rested on his palm. It was the strangest sensation; she was obviously more substantial than any hologram. He could feel something warm and soft that resembled skin but made his hand tingle as if there was a light electrical current running through it. They stood like that for some time before Amanda pulled away.

"You'd better head to the infirmary or you'll miss Colonel Young." Rush nodded and turned to go but stopped and turned back.

"Will I see you again soon?"

"Of course. We have a lot of catching up to do." She smiled warmly.

"I've really missed you Mandy."

"I know. I've missed you too. Now go and meet Colonel Young." He nodded and turned to go but her voice stopped him. "Nick? I just wanted to let you know the ship will be fine until we reach the star system. The alarms were just me messing with Brody and Volker. I thought you might appreciate that."

He smiled at her and headed to the infirmary leaving Amanda alone. She let her smile fade after he was out of sight and took a moment as if to brace herself before disappearing.

Rush met up with Colonel Young in the hall a ways from the infirmary and the fell into step together.

"Rush, I was just about to call you."

"Well, I had a break in what I was able to do, so I thought it might be a good time to drop by and see how Eli is doing. I need to ask him a few questions as well."

"Go easy on him Rush. Poor kid looks like he's been through hell." They entered the infirmary to see T.J. standing by Eli's bed helping him with a cup of water. Her back was to them when they entered so Eli saw them first. He coughed and choked on the water he'd just inhaled and it was a moment or two before he was alright to speak. He smiled weakly up at them and Rush could see that he was in pretty rough shape. Dark purple circles under his eyes betrayed his complete exhaustion. He looked as if he'd carried the weight of the universe on his shoulders before going into stasis and had tried to pick it up again after he'd come out. There were several patches of damaged skin visible that looked like burns and deep worry lines marred his once youthful face making him look drawn and so much older.

Rush approached slowly. "Hello Eli."

Eli watched him warily. "Rush." His voice sounded ragged. T.J. stood beside him protectively, giving Rush a very similar look.

Rush ignored her. "How are you feeling?"

"Like I went through hell. Which I suppose is a pretty accurate description of what happened."

"Yeah, you certainly look it." Rush glanced at T.J. and Young before continuing. "I'd like to discuss some business matters if you're feeling up to it."

"Actually Rush, I need to debrief Eli first. If he's up to talking after that−"

"No, Colonel."

"What?"

"Please give us a few minutes Colonel. You too T.J. I'll be fine." He spoke without looking at either of them. He stared at Rush like he was waiting for a venomous snake to strike.

Young grudgingly nodded. "Alright, we'll be right outside. Call if you need anything." Rush watched them leave before pulling a chair up to Eli's bedside, sinking into it with a relieved sigh. He sat back and the two watched each other in silence. Finally, Rush leaned forward, elbows on his knees, and looked at Eli intently.

"Eli, we need to talk about Dr. Amanda Perry."

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><p><strong>A.N. Hey guys! I cannot say how sorry I am that it took me this long to post another chapter, but my life kind of got in the way. I want to continue this story, but I unfortunately don't know when I will be able to post the next chapter. The school year is coming up and I'm going to be very busy again very soon.<strong>

**I wanted to thank billandsookie, LetsTwistAnotherFairyTale, Serena Thorn, BookBrink, wintersmith, a. , Opera123, R2R, Destiny001, and cat4444 for their wonderful reviews. I also want to thank anyone who has Favorited or put me on story alert. Your support has been wonderful!**

**I hope you all enjoyed this chapter. Remember, reviews are love! Thank you all again for reading this, and I'll see you at the next chapter whenever that may be.**


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